Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1DFO

CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004372	molecular_function	glycine hydroxymethyltransferase activity
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006545	biological_process	glycine biosynthetic process
A	0006546	biological_process	glycine catabolic process
A	0006564	biological_process	L-serine biosynthetic process
A	0006565	biological_process	L-serine catabolic process
A	0006730	biological_process	one-carbon metabolic process
A	0008270	molecular_function	zinc ion binding
A	0008652	biological_process	amino acid biosynthetic process
A	0008732	molecular_function	L-allo-threonine aldolase activity
A	0016020	cellular_component	membrane
A	0016740	molecular_function	transferase activity
A	0019264	biological_process	glycine biosynthetic process from serine
A	0030170	molecular_function	pyridoxal phosphate binding
A	0035999	biological_process	tetrahydrofolate interconversion
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0046653	biological_process	tetrahydrofolate metabolic process
B	0004372	molecular_function	glycine hydroxymethyltransferase activity
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006545	biological_process	glycine biosynthetic process
B	0006546	biological_process	glycine catabolic process
B	0006564	biological_process	L-serine biosynthetic process
B	0006565	biological_process	L-serine catabolic process
B	0006730	biological_process	one-carbon metabolic process
B	0008270	molecular_function	zinc ion binding
B	0008652	biological_process	amino acid biosynthetic process
B	0008732	molecular_function	L-allo-threonine aldolase activity
B	0016020	cellular_component	membrane
B	0016740	molecular_function	transferase activity
B	0019264	biological_process	glycine biosynthetic process from serine
B	0030170	molecular_function	pyridoxal phosphate binding
B	0035999	biological_process	tetrahydrofolate interconversion
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0046653	biological_process	tetrahydrofolate metabolic process
C	0004372	molecular_function	glycine hydroxymethyltransferase activity
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006545	biological_process	glycine biosynthetic process
C	0006546	biological_process	glycine catabolic process
C	0006564	biological_process	L-serine biosynthetic process
C	0006565	biological_process	L-serine catabolic process
C	0006730	biological_process	one-carbon metabolic process
C	0008270	molecular_function	zinc ion binding
C	0008652	biological_process	amino acid biosynthetic process
C	0008732	molecular_function	L-allo-threonine aldolase activity
C	0016020	cellular_component	membrane
C	0016740	molecular_function	transferase activity
C	0019264	biological_process	glycine biosynthetic process from serine
C	0030170	molecular_function	pyridoxal phosphate binding
C	0035999	biological_process	tetrahydrofolate interconversion
C	0042802	molecular_function	identical protein binding
C	0042803	molecular_function	protein homodimerization activity
C	0046653	biological_process	tetrahydrofolate metabolic process
D	0004372	molecular_function	glycine hydroxymethyltransferase activity
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006545	biological_process	glycine biosynthetic process
D	0006546	biological_process	glycine catabolic process
D	0006564	biological_process	L-serine biosynthetic process
D	0006565	biological_process	L-serine catabolic process
D	0006730	biological_process	one-carbon metabolic process
D	0008270	molecular_function	zinc ion binding
D	0008652	biological_process	amino acid biosynthetic process
D	0008732	molecular_function	L-allo-threonine aldolase activity
D	0016020	cellular_component	membrane
D	0016740	molecular_function	transferase activity
D	0019264	biological_process	glycine biosynthetic process from serine
D	0030170	molecular_function	pyridoxal phosphate binding
D	0035999	biological_process	tetrahydrofolate interconversion
D	0042802	molecular_function	identical protein binding
D	0042803	molecular_function	protein homodimerization activity
D	0046653	biological_process	tetrahydrofolate metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	20
Details	BINDING SITE FOR RESIDUE PLG A 1001

Chain	Residue
A	SER35
A	HIS203
A	THR226
A	HIS228
A	LYS229
A	ARG363
A	FFO1002
B	TYR55
B	TYR65
B	GLY262
B	GLY263
A	SER97
B	HOH500
A	GLY98
A	SER99
A	HIS126
A	PHE174
A	SER175
A	ASP200
A	ALA202

site_id	AC2
Number of Residues	23
Details	BINDING SITE FOR RESIDUE FFO A 1002

Chain	Residue
A	LEU121
A	GLY125
A	HIS126
A	LEU127
A	SER175
A	ASN347
A	SER355
A	PRO356
A	PHE357
A	HOH664
A	HOH694
A	HOH787
A	HOH859
A	PLG1001
B	GLU57
B	TYR64
B	TYR65
B	PHE257
B	HOH530
B	HOH961
D	SER245
D	GLU246
D	GLU247

site_id	AC3
Number of Residues	21
Details	BINDING SITE FOR RESIDUE PLG B 2001

Chain	Residue
A	TYR55
A	TYR65
A	GLY262
A	GLY263
A	HOH506
A	HOH548
B	SER35
B	SER97
B	GLY98
B	SER99
B	HIS126
B	PHE174
B	SER175
B	ASP200
B	ALA202
B	HIS203
B	THR226
B	HIS228
B	LYS229
B	ARG363
B	FFO2002

site_id	AC4
Number of Residues	17
Details	BINDING SITE FOR RESIDUE FFO B 2002

Chain	Residue
A	GLU57
A	TYR64
A	TYR65
A	PHE257
A	HOH548
B	LEU121
B	GLY125
B	HIS126
B	LEU127
B	SER175
B	ASN347
B	SER355
B	PRO356
B	PHE357
B	HOH763
B	HOH791
B	PLG2001

site_id	AC5
Number of Residues	20
Details	BINDING SITE FOR RESIDUE PLG C 3001

Chain	Residue
D	GLY263
D	HOH504
C	SER35
C	SER97
C	GLY98
C	SER99
C	HIS126
C	PHE174
C	SER175
C	ASP200
C	ALA202
C	HIS203
C	THR226
C	HIS228
C	LYS229
C	ARG363
C	FFO3002
D	TYR55
D	TYR65
D	GLY262

site_id	AC6
Number of Residues	18
Details	BINDING SITE FOR RESIDUE FFO C 3002

Chain	Residue
B	SER245
B	GLU246
B	GLU247
C	LEU121
C	GLY125
C	HIS126
C	LEU127
C	SER175
C	ASN347
C	SER355
C	PRO356
C	PHE357
C	HOH656
C	PLG3001
D	GLU57
D	TYR64
D	TYR65
D	PHE257

site_id	AC7
Number of Residues	20
Details	BINDING SITE FOR RESIDUE PLG D 4001

Chain	Residue
C	TYR55
C	TYR65
C	GLY262
C	GLY263
C	HOH505
D	SER35
D	SER97
D	GLY98
D	SER99
D	HIS126
D	PHE174
D	SER175
D	ASP200
D	ALA202
D	HIS203
D	THR226
D	HIS228
D	LYS229
D	ARG363
D	FFO4002

site_id	AC8
Number of Residues	18
Details	BINDING SITE FOR RESIDUE FFO D 4002

Chain	Residue
C	GLU57
C	TYR64
C	TYR65
C	PHE257
C	HOH525
D	LEU121
D	GLY125
D	HIS126
D	LEU127
D	SER175
D	ASN347
D	SER355
D	PRO356
D	PHE357
D	HOH674
D	HOH675
D	HOH1027
D	PLG4001

Functional Information from PROSITE/UniProt

site_id	PS00096
Number of Residues	17
Details	SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. HVvTTTTHKTLaGPRGG

Chain	Residue	Details
A	HIS221-GLY237

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	32
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10656824","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"10858298","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1DFO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EQB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10656824","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1DFO","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00051","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10656824","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"10858298","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1DFO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EQB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19883126","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3G8M","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Site: {"description":"Transaldimination and stability"}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Site: {"description":"Plays an important role in substrate specificity","evidences":[{"source":"HAMAP-Rule","id":"MF_00051","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"1517215","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	24
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"PubMed","id":"21151122","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"HAMAP-Rule","id":"MF_00051","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19883126","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3G8M","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	8
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"21151122","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)